# Predict Synthetic Lethality and Other Gene Dependency Relationships from Multiomics Data

## Documentation for package ‘MultiSEp’ version 4.1.3

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

depMapCRISPRscores_subset | Example CRISPR score input matrix
depMapMUT_small | Example mutation data input matrix
depMapMUT_subset | Example mutation data input matrix
depMapTissue_subset | Example tissue data input matrix
depMapXPR_small | Example gene expression input matrix
depMapXPR_subset | Example gene expression input matrix
Formatted_MUTimpactMatrix | The output of 'mts_formatMatrix()' function for an example dataset.
mixModelClusters_depMapCRISPR | Clusters of samples (cell lines) from the 'mts_mixModelCluster' function for a small dataset of DepMap CRISPR scores.
mixModelClusters_depMapXPR | Clusters output from the 'mts_mixModelCluster' function for a toy DepMap expression dataset.
mixModelClusters_vignette | Clusters output from the 'mts_mixModelCluster' function for a DepMap expression data that is required for the vignette.
mRes | Example results for the 'mts_Mutation' function.
mts_clusterAvg | Determine average CRISPR score values for gene expression clusters
mts_Crispr | Investigate Gene Dependency Relationships with CRISPR and gene expression data
mts_crisprPartition | Partition CRISPR gene effect scores
mts_CrisprTS | Predict tissue-specific gene dependency relationships, evaluating differences in CRISPR scores for gene A between expression clusters for gene B (SynLeGG).
mts_formatMatrix | Format a matrix into a list of data frames that capture gene functional status
mts_GeneDepCrispr | CRISPR and gene expression gene-dependency prediction (SynLeGG)
mts_GeneDepID | CRISPR vs gene expression induced dependency pipeline (SynLeGG)
mts_GeneDepMutation | Mutation vs gene expression gene-dependency prediction
mts_genepairsChunkGeneration | Generate '.RData' files containing subsets of gene pairs
mts_InducedDependency | Predict 'induced dependency' relationships, evaluating differences in CRISPR scores for gene A between expression clusters for gene B
mts_mixModelCluster | Cluster continuous data with Gaussian Mixture Modelling
mts_mixModelCluster_XPR | Cluster gene expression data with Gaussian Mixture Modelling
mts_Mutation | Integrate gene cluster assignments with mutation data
mts_omics | Predict synthetic lethality and other dependency relationships from mutually exclusive loss of function patterns
mts_pairwiseExpressionPlot | Visualise pairwise gene expression data with MultiSEp cluster boundaries.
mts_patternDetection | Predict Gene Dependency Relationship Patterns, including Synthetic Lethality
mts_plotClusterDistribution | Visualise samples and pairwise gene expression clusters
mts_plotCRISPRGeneCluster | Visualise CRISPR and expression data (SynLeGG methods).
mts_plotMutation | Visualise clusters for one gene with the mutation status of another gene.
mts_targetCoverageFromMutations | Predict the therapeutic population coverage achieved by inhibition of a candidate target gene
mts_tests | Unit Tests for the MultiSEp package
multisepCrisprList | Example Multisep t-test CRISPR vs XPR results object.
multisepList | Example results from mts_clusterAvg()
MUT_impactMatrix | Example mutation impact matrix